User: hongbo919

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hongbo91920
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Posts by hongbo919

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Comment: C: How to get some result in WGBS?
... Hi, for the 2nd, you can try the absolute difference larger than 0.3. If you have more samples without replicates, you can try the Entropy-based methods such as QDMR (http://fame.edbc.org/qdmr/) or SMART (http://fame.edbc.org/smart/), both of them can process such kind of situation. ...
written 9 months ago by hongbo91920
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Answer: A: Multisample DMR calling
... Hi Aerval, we have developed a new software (SMART-BS-Seq) for de novo identification of DMRs from various BS-Seq data including WGBS. I think this software is what you are looking for. SMART-BS-Seq can identify the group-specific DMRs across multiple groups without pairwise comparisons. Detailed in ...
written 9 months ago by hongbo91920
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Answer: A: Assessing DMRs between treatment groups: subtracting control group DMRs to accou
... I suggest using the DMR identification software based on entropy such [QDMR][1] (for pre-defined regions) or [SMART][2] (for de novo identification of DMRs from BS-Seq data). As there are multiple samples in the same group, the DMC function of [SMART][3] should work for your project. [1]: http:/ ...
written 13 months ago by hongbo91920
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Answer: A: Methylation Analysis (Bisulfite sequencing)
... Hi, we have developed a new software for de novo identification of DMRs from various BS-Seq data including WGBS. Maybe it is useful for you. [http://fame.edbc.org/smart/][1] Best wishes! :) [1]: http://fame.edbc.org/smart/ ...
written 13 months ago by hongbo91920
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Answer: A: Differential Methylation in specific groups
... What I guess is that your want to identify the group-specific DMRs from EPIC data. I suggest using the DMR identification software based on entropy such [QDMR][1] (for pre-defined regions) or [SMART][2] (for de novo identification of DMRs from BS-Seq data). As there are multiple samples in the same ...
written 13 months ago by hongbo91920
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Answer: A: Functional analysis of differential methylation regions
... Due the methylation data ranges from 0(unmethylated) to 1(fully methylated). Thus, we always don't use log-fold change although it is always used in gene expression analysis. We suggest using the DMR identification software such [QDMR][1] (for pre-defined regions) or [SMART][2] (for de novo identifi ...
written 13 months ago by hongbo91920
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Answer: A: Differential Methylation Analysis
... Hi, we have developed a new software for de novo identification of DMRs from various BS-Seq data including WGBS. Maybe it is useful for you. [http://fame.edbc.org/smart/][1] Best wishes! :) [1]: http://fame.edbc.org/smart/ ...
written 13 months ago by hongbo91920
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Answer: A: Dmr (Differentially Methylated Regions) Identification Software
... Hi, we have developed a new software for de novo identification of DMRs from various BS-Seq data including WGBS. Maybe it is useful for you. [http://fame.edbc.org/smart/][1] Best wishes! :) [1]: http://fame.edbc.org/smart/ ...
written 13 months ago by hongbo91920

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